A petition from him to the supreme council shows that he had no pay for eighteen months, except 200l. during the siege of Duncannon. The very expenses of his outfit and passage from Flanders had not been paid. The supreme council acknowledged on 2 May 1645 that they owed him 1,300l., which they ordered to be paid out of the rents due to the crown at Easter and Michaelmas that same year (ib. p. 239). As to the rest of his arrears, they would settle them at some more convenient season, ‘as shall be agreeable to honour and justice.’ In October Preston was sent to reduce Youghal, but he quarrelled with his colleague Castlehaven, and the expedition failed.
Preston was one of two deputed by the supreme council to wait upon the nuncio, Rinuccini, who brought over arms, ammunition, and money, after his arrival at Kilkenny in the middle of November. The nuncio distrusted every one, and, after much dispute, agreed to allot half the fund at his disposal to Connaught, where Clanricarde found it hard to maintain his ground. In April 1646 Preston was despatched to his help with three thousand foot and five hundred horse, and the nuncio said his readiness ‘to serve under Clanricarde had edified all, and given the best hopes of good service from him.’ Preston took Roscommon about the time of the battle of Benburb (5 June) (Warr of Ireland, p. 56), and gained some success in the field. But his jealousy of Owen Roe O'Neill threatened a dangerous development, and Owen Roe, anxious to spare his own province of Ulster, allowed some of his victorious but hungry troops to spread themselves over the counties of Westmeath and Longford, where they committed many excesses. Preston's men were largely drawn from that district, and disturbances were imminent (Confederation and War, v. 32). Rinuccini made peace between the rival generals, but it was neither real nor lasting.
A peace was concluded in March 1646 between Ormonde and the confederates, but it did not put an end to the war. Preston, who was in Connaught till October, had a natural leaning towards Ormonde, and, after a friendly correspondence with him, proclaimed the peace in camp. But he was afterwards over-persuaded by Rinuccini to reopen the war by joining O'Neill in an attack on Dublin. At the end of August Ormonde had gone to Kilkenny, where he collected some of his rents. A determined attempt was now made to cut him off from the capital. He escaped with his men by forced marches, but his baggage was plundered by the Irish. He saw that the confederates could not be trusted, and suspected Preston equally with O'Neill of complicity in this breach of faith. Ormonde saw that the protestants of Dublin and of the other garrisons could only be saved by the help of the English parliament. On 9 Nov. Preston, O'Neill, and Rinuccini were together at Lucan, only seven miles from Dublin; but the generals quarrelled so violently that the nuncio had much ado to keep them from actually coming to blows. At the news that Ormonde was treating with the parliamentarians, O'Neill suddenly recrossed the Liffey and left Preston alone. Preston's position was very difficult. On 21 Oct. he swore allegiance to the ‘council and congregation of the confederates,’ that is, to the clerical section who were now in power at Kilkenny; but a few days later, at the persuasion of Clanricarde, he accepted, with some hesitation, Ormonde's assurances that by maintenance of peace his co-religionists would gain full religious liberty. In a letter dated 24 Nov. to the mayor and citizens of Kilkenny he spoke triumphantly of the extension of the catholic religion, and the restriction of heresy in Leinster to Dublin, Drogheda, Dundalk, and Trim, while he complained bitterly that his plan of besieging Dublin and thus extorting catholic emancipation had been hampered by tempest and flood, and that his desertion by O'Neill had now exposed him and his men to great peril (see Confederation and War, vi. 162).
He adhered to his understanding with Clanricarde only until December. The nuncio early in that month excommunicated Preston for refusing to disperse his army in quarters assigned by the clerical party at Kilkenny. A few days later he renewed his promises of obedience to the church and repudiated the understanding with Clanricarde. He had just proposed a friendly meeting with Ormonde, but excused himself on the ground that his officers were ‘not excommunication proof’ (ib. pp. 45, 167). A truce with Ormonde was maintained until 10 April. On the very night that it ended Preston invested the royalist garrison at Carlow. It fell into his hands three weeks later, but to little purpose, for a parliamentary army under Michael Jones [q. v.] was admitted into Dublin on 7 June, and on 28 July Ormonde left Ireland, just when Preston was mustering seven thousand foot and a thousand horse on the Curragh of Kildare.
Jones attacked him at Dangan Hill, near Trim, on 8 Aug., and his army was almost annihilated (Jones's account in Rushworth, vii. 779; Rinuccini, p. 306; Contemporary Hist. i. 154).
The defeated general retired to Kilkenny